Align Probable 5-dehydro-4-deoxyglucarate dehydratase; EC 4.2.1.41; 5-keto-4-deoxy-glucarate dehydratase; KDGDH (uncharacterized)
to candidate Pf1N1B4_3332 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7)
Query= curated2:A4YNH1 (314 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3332 Length = 292 Score = 92.8 bits (229), Expect = 9e-24 Identities = 85/278 (30%), Positives = 126/278 (45%), Gaps = 19/278 (6%) Query: 22 VTPFKADYSFDETTYRSNMDWLCGYDVAGLFAAGGTGEFFSLTAAEVPEVVKVAVDETKG 81 VTP A D + +D+ + A G TGE +L E EV++ V + G Sbjct: 10 VTPMDAQGRLDWDSLSKLVDFHLQEGTNAIVAVGTTGESATLDVNEHIEVIRRVVAQVAG 69 Query: 82 RVPVLAGTGYG-TAIAREIAMSAEKAGADGLLLLPPYLMHAEQEGLAAHVEAVCKSVKIG 140 R+PV+AGTG T A E+ +A+ AGAD LL+ PY QEGL H +A+ ++V I Sbjct: 70 RIPVIAGTGANSTREAIELTTNAKNAGADACLLVTPYYNKPTQEGLYQHFKAIAEAVDIP 129 Query: 141 VIVYN---RDNAILQPDTLARLCERCPNLVGYKDGIGDIELMTRVYTKM-GDRLTYIGGL 196 I+YN R +Q +T+ RL N++G K+ GD++ + + D L Y G Sbjct: 130 QILYNVPGRTACDMQAETVIRL-STVKNIIGIKEATGDLQRAKDILAGVSSDFLVYSGDD 188 Query: 197 PTAETFALPYLDMGVTTYSSAVFNFVPEFATNFYAAVRKRDHATIHAGLKDFILPLIAIR 256 TA L +G S N P + AA D A + + ++PL Sbjct: 189 ATAVELML----LGGKGNISVTANVAPRAMSELCAAAMAGDAVKARA-IHEKLMPL---- 239 Query: 257 NRKKGYAVS---IIKAGMKVIGRDSGPVRLPLTDLTEA 291 K + S +K + +G +RLPLT L+ A Sbjct: 240 -NKTLFIESNPIPVKWALHEMGLMPDGIRLPLTWLSAA 276 Lambda K H 0.320 0.136 0.392 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 206 Number of extensions: 11 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 314 Length of database: 292 Length adjustment: 27 Effective length of query: 287 Effective length of database: 265 Effective search space: 76055 Effective search space used: 76055 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory